Research workbench
Crystal structure analysis of fungal versatile peroxidase from pleurotus eryngii
Analyse Crystal structure analysis of fungal versatile peroxidase from pleurotus eryngii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FJW
- Type
- protein
- Length
- 662 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Versatile peroxidase VPL2
- EC
- 1.11.1.16
- UniProt
- O94753
- Ligands
- HEM, MAN, BMA, NAG, CA, MN
- Pockets
- 4 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Versatile peroxidase VPL2 (EC 1.11.1.16) | protein | 331 | 39% helix, 7% strand | O94753 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 8 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 428 | 0.82 | 0.90 | 41 | HEM |
| 2 | 406 | 0.81 | 0.89 | 50 | HEM, MN |
| 3 | 538 | 0.64 | 0.76 | 57 | MAN |
| 4 | 52 | 0.24 | 0.73 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 697 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 glycan, 8 disulfide (disulfide, O-glycosylation, N-glycosylation).
Compared structures
- 3FJW · Crystal Structure Analysis of Fungal Versatile Peroxidase from Pleurotus eryngii · the same entry in another collection · chain A against A, TM-score 1.00
- O94753 · AlphaFold monomer V2.0 prediction for versatile peroxidase VPL2 (O94753) · a predicted model of the same protein · chain A against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt O94753
- Elsewhere: RCSB PDB 3FJW · PDBe 3FJW · UniProt O94753
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